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DNA analysis of an early modern human from Tianyuan Cave, China
Open accessAbstract
Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.
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“We evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide29, by requiring that the ratio of X-to-Y-chromosome sequences was characteristic of either a male or a female, by requiring >95% matching to the consensus sequence of mitochondrial DNA30, and by requiring (for males) a lack of variation”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [30]
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“We assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [30]
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“pestis captures of both full-UDG and partially-UDG-treated libraries were performed using a published protocol (Fu et al., 2013), adapted for Y.”
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Self-citationA Robust Framework for Microbial Archaeology
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“This technique can be performed either on chip (20) or in solution (9, 52), and the goal is to remove unwanted DNA from a sample prior to sequencing.”
BackgroundSelf-citationAncient DNA reveals a multistep spread of the first herders into sub-Saharan Africa
Prendergast, M. E., Lipson, M., Sawchuk, E., Olalde, Í., Ogola, C. A., Rohland, N., Sirak, K. A., Adamski, N., Bernardos, R. L., Broomandkhoshbacht, N., et al. (2019) · Science · doi:10.1126/science.aaw6275 · Cited by 204
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Late Pleistocene archaic human crania from Xuchang, China
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Self-citationThe Demographic Development of the First Farmers in Anatolia
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The evolutionary history of Neanderthal and Denisovan Y chromosomes
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Craniometrics Reveal “Two Layers” of Prehistoric Human Dispersal in Eastern Eurasia
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Harnessing ancient genomes to study the history of human adaptation
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“Fu et al.(171) 2013 1 1 Chromosome 21 capture South and central Asia 1”
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Self-citationHunter-Gatherers and the Origins of Religion
Peoples, H. C., Duda, P., & Marlowe, F. W. (2016) · Human Nature · doi:10.1007/s12110-016-9260-0 · Cited by 186
“Pleistocene hunter-gatherers would most likely have possessed both the cognitive and communicative skills to share religious beliefs and practices prior to dispersal out of Africa more than 60 kya (Fu et al. 2013; Henn et al. 2012; Johansson 2011; Lind et al. 2013).”
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Self-citationBeringia and the global dispersal of modern humans
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“The capture was performed as previously described (62) on 96604 well plates with a maximum of two samples pooled per well and all blanks with unique index 605”
Inferences from tip‐calibrated phylogenies: a review and a practical guide
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The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomesPreprint
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“2015 with the advent of large-scale studies of Holocene genomes, in-solution enrichment of ancient DNA libraries for targeted single nucleotide polymorphisms (SNPs) [4-6] and the introduction of automated protocols and liquid handling robots for processing of ancient DNA libraries [7, 8], that the number of individual…”
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A working model of the deep relationships of diverse modern human genetic lineages outside of Africa
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“The former includes present-day East Asians and had differentiated as early as the 40 kya Tianyuan individual (Fu et al. 2013), while early members of the latter include ancient European hunter-gatherers (Lazaridis et al.”
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“The baits were then cleaved, amplified, and biotinylated in preparation for enrichment (Fu et al. 2013).”
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“2 million SNPs was performed using a set of DNA capture probes [“1240k”, composed of SNP panels 1 and 2, as described elsewhere (45)] and two successive rounds of in-solution hybridization capture (75).”
MethodSelf-citationResolving the ancestry of Austronesian-speaking populations
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“Ancient DNA calibration is becoming a widely used approach (Ho et al. 2007), but estimates based on a single sequence are highly divergent and present large confidence intervals (Fu et al. 2013b).”
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“However, we now know that Neanderthals and Denisovans (and potentially other archaic lineages) are part of many peoples’ ancestry today, raising the question of whether it is valid to exclude them from our species.”
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The source of the Black Death in fourteenth-century central Eurasia
Spyrou, M. A., Musralina, L., Gnecchi‐Ruscone, G. A., Kocher, A., Borbone, P. G., Khartanovich, V. I., Buzhilova, A., Djansugurova, L., Bos, K. I., Kühnert, D., et al. (2022) · Nature · doi:10.1038/s41586-022-04800-3 · Cited by 160
Metadata
- Authors
- Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S.
- Affiliations
- Max Planck Society (DE)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Max Planck Institute for Developmental Biology (DE)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-01-22
- Volume
- 110
- Issue
- 6
- Pages
- 2223-2227
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3568306
- OpenAlex
- W2149683346
- Cited by
- 608
- References
- 47
- Citations by year
- 2026: 27 · 2025: 52 · 2024: 45 · 2023: 45 · 2022: 45 · 2021: 78 · 2020: 64 · 2019: 35 · 2018: 49 · 2017: 43 · 2016: 38 · 2015: 35 · 2014: 34 · 2013: 17
- FWCI
- 27.40
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- early modern humans, ancient DNA, mitochondrial genome, nuclear genome, chromosome 21, archaic admixture, Asian ancestry, Native American ancestry
- MeSH terms
- Animals, Base Sequence, China, Chromosomes, Human, Pair 21, DNA, Mitochondrial, Fossils, Genetics, Population, Humans, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid, Hominidae, Gene Library, Sequence Analysis, DNA, Asian People, History, Ancient, Phylogeography
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